What is your chosen design software?
Looks like you have 3 operations for each token? Anything on the other side?
Assuming 3 operations on one side, there should only be 3 thumbnails on the side bar. One for each engrave and one for the cut. I’m just wondering where the other thumbnails come from.
I did two jobs of 1,000 tokens each engraved on both sides, and I discovered a couple of things. A full sheet of tokens exceeded the buffer capacity at more than three hours, so like you, I needed to reduce the number of tokens in each run. Lowering the resolution from 270 LPI to 225 produced acceptable detail while reducing the required time and buffer load. The reduced run time saved me like 4 hours across each job.
Also, because the full sheet of 20x12 can’t be reached, I broke the file into two and cut the sheet almost in half on a miter saw so that I could use the whole sheet.
My file also had some seemingly odd motion planning, doing row after row sequentially but skipping 4 over here and 3 over there, but it would return to them and finish.
There are some design software wizards around here that could look at your file and eliminate that as a potential problem if you could zip it and post it here.
Regarding the incomplete cuts, with proofgrade material and settings, the company has been good about crediting accounts for failures.
Another detail that can help support figure this out is including the date, time and time zone in the report so they can review the machine logs.